Fig. 1b

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Fig 1c

Genes detected

Fig 1d

Sample Correlation Matrix

Fig 1e-h

PCA Plots (using all genes)

3d plot

PC Median Heatmaps

Figure 1-1

Distribution of mean TPM by stage

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Figure 1-2

PCA Matrix Plot

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Figure 1-3

DETCT Sample QC plot

Figure 1-4

DETCT PCA

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Figure 3

Fig3A

Max Stage Clusters TPM heatmap

ZFA enrichment

Figure 3-1

Orthologues of Named/Unnamed genes

Named Genes

Unnamed Genes

Figure 4

Cluster Chromosome Count Expected log2FE Adjusted.pvalue
Cluster023 Chr1 9 2.25 2.00 1.161e-02
Cluster004 Chr4 129 47.29 1.45 7.434e-24
Cluster022 Chr4 14 5.03 1.48 1.156e-02
Cluster037 Chr4 23 3.35 2.78 9.033e-14
Cluster084 Chr4 9 1.48 2.61 1.659e-04
Cluster074 Chr12 8 0.48 4.05 6.337e-07

Table showing clusters with significant chr enrichments (adjusted p-value < 0.05 and log2 fold change > 1).

Chr 4 Zinc Finger Genes

Cluster Freq
4 Cluster004 121
37 Cluster037 18
22 Cluster022 14
84 Cluster084 6

Table showing the numbers of chromosome 4 zinc finger genes in the biolayout clusters (more than 5 in a cluster).

Chr 4 ZnF enrichment

The table below shows the clusters with enrichments significantly larger than expected by chance for the chromosome 4 zinc finger genes.

Cluster Category Count Expected log2FE pvalue adjusted.pvalue
Cluster004 Chr4ZnF 121 8.34 3.86 4.243e-100 2.546e-99
Cluster022 Chr4ZnF 14 0.89 3.98 1.608e-13 9.647e-13
Cluster037 Chr4ZnF 18 0.59 4.93 3.500e-23 2.100e-22
Cluster084 Chr4ZnF 6 0.26 4.53 1.201e-07 7.206e-07

Table showing clusters with significant enrichments (adjusted p-value < 0.05).

Fig4A

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Fig4C - NLR genes tpm heatmap

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Fig4D - Chr22 Znf genes tpm heatmap

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Fig4E - Chr4 tpm heatmap

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Fig4F-G - histograms of ZnF/NLR genes on chr 4

Histogram showing the distribution of genes in clusters 4, 22, 37 and 84.

Histogram showing the distribution of NLR genes on chromosome 4 (binwidth = 5 Mb).

Figure 4-2

histograms of ZnF genes on chr 4, split by cluster

Histogram showing the distribution of genes in clusters 4, 22, 37 and 84, split by cluster.

Regional expression

Figure 4-3A

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Figure 5

Fig5A

Pearson histogram (Paralogues)

Histogram of Pearson coefficients between paralogous gene pairs (binwidth = 0.1)

Fig5B

Pearson histogram (random sample)

Histogram of Pearson coefficients of a random selection of 3000 genes pairs.

Fig5C

top10/bottom10 tpm heatmap

Fig5D-G

scatterplots/point based expression profiles

Fig.6C

Count bar chart by Stage

Session Info

## R version 3.3.1 (2016-06-21)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.11.6 (El Capitan)
## 
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] rgl_0.96.0                 qvalue_2.4.2              
##  [3] genefilter_1.54.2          DESeq2_1.12.4             
##  [5] SummarizedExperiment_1.2.3 htmlTable_1.6             
##  [7] biomaRt_2.28.0             Rgraphviz_2.16.0          
##  [9] gridExtra_2.2.1            topGO_2.24.0              
## [11] SparseM_1.7                GO.db_3.3.0               
## [13] graph_1.50.0               cba_0.2-17                
## [15] proxy_0.4-16               RColorBrewer_1.1-2        
## [17] plyr_1.8.4                 GenomicFeatures_1.24.5    
## [19] AnnotationDbi_1.34.4       Biobase_2.32.0            
## [21] GenomicRanges_1.24.2       GenomeInfoDb_1.8.3        
## [23] IRanges_2.6.1              S4Vectors_0.10.3          
## [25] BiocGenerics_0.18.0        scales_0.4.0              
## [27] reshape2_1.4.1             ggplot2_2.1.0             
## [29] rprojroot_1.0-2            knitr_1.14                
## 
## loaded via a namespace (and not attached):
##  [1] jsonlite_1.0            splines_3.3.1          
##  [3] Formula_1.2-1           shiny_0.13.2           
##  [5] highr_0.6               latticeExtra_0.6-28    
##  [7] Rsamtools_1.24.0        yaml_2.1.13            
##  [9] RSQLite_1.0.0           lattice_0.20-33        
## [11] chron_2.3-47            digest_0.6.10          
## [13] XVector_0.12.1          colorspace_1.2-6       
## [15] httpuv_1.3.3            htmltools_0.3.5        
## [17] Matrix_1.2-6            XML_3.98-1.4           
## [19] zlibbioc_1.18.0         xtable_1.8-2           
## [21] BiocParallel_1.6.6      annotate_1.50.0        
## [23] nnet_7.3-12             mime_0.5               
## [25] survival_2.39-5         magrittr_1.5           
## [27] evaluate_0.9            foreign_0.8-66         
## [29] tools_3.3.1             data.table_1.9.6       
## [31] formatR_1.4             matrixStats_0.50.2     
## [33] stringr_1.1.0           munsell_0.4.3          
## [35] locfit_1.5-9.1          cluster_2.0.4          
## [37] Biostrings_2.40.2       RCurl_1.95-4.8         
## [39] htmlwidgets_0.7         labeling_0.3           
## [41] bitops_1.0-6            rmarkdown_1.0          
## [43] gtable_0.2.0            DBI_0.5                
## [45] R6_2.1.3                GenomicAlignments_1.8.4
## [47] rtracklayer_1.32.2      Hmisc_3.17-4           
## [49] stringi_1.1.1           Rcpp_0.12.6            
## [51] geneplotter_1.50.0      rpart_4.1-10           
## [53] acepack_1.3-3.3